Added an abyss component to flowcraft, and added a new disableRR parameter to spades#146
Added an abyss component to flowcraft, and added a new disableRR parameter to spades#146ODiogoSilva merged 21 commits intoassemblerflow:devfrom
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Codecov Report
@@ Coverage Diff @@
## dev #146 +/- ##
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+ Coverage 38.92% 38.97% +0.04%
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Files 59 59
Lines 5636 5647 +11
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+ Hits 2194 2201 +7
- Misses 3442 3446 +4
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ODiogoSilva
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ODiogoSilva
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Great contribution @emreerhan! Very thorough with the addition of logging and documentation for new parameters 👍 I've only added one simple comment. Will also change the PR to dev instead of master as this is common practice in flowcraft. We only merge to master for new releases.
| self.input_type = "fastq" | ||
| self.output_type = "fasta" | ||
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| # self.dependencies = ["integrity_coverage"] |
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It's OK to remove this line altogether
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Nice work, just had some minor comments. Maybe @ODiogoSilva has something to say about the spades modifications but they looked fine to me.
| self.input_type = "fastq" | ||
| self.output_type = "fasta" | ||
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| # self.dependencies = ["integrity_coverage"] |
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Do you need this line? If you don't need it, remove it.
| "true_coverage": readsqc.TrueCoverage, | ||
| "viral_assembly": assembly.ViralAssembly | ||
| "viral_assembly": assembly.ViralAssembly, | ||
| "abyss": assembly.Abyss |
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Although this will probably be refactored according to #145 , can you keep the alphabetical order for now?
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I accidentally pushed my changes to |
emreerhan
changed the title
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Yes, there is one more thing. Could add these changes to the |
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Sooooorry @emreerhan 😅 Could you put the change log entries in the |
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Oops! |
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Welcome to the team @emreerhan 💪 The docker image for abyss will also be up in dockerhub shortly, after the PR is merged. |
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Good job and welcome to the team @emreerhan . Very nice PR. Hope you have fun with FlowCraft! |
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